A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
/home/runner/work/pmultiqc/pmultiqc/data
pmultiqc
pmultiqc is a MultiQC module to show the pipeline performance of mass spectrometry based quantification pipelines such as nf-core/quantms, MaxQuant, and DIA-NN.URL: https://github.com/bigbio/pmultiqc
Experimental Design and Metadata
Experimental Design
| Sample Name | MSstats Condition | MSstats BioReplicate | Fraction Group | Fraction | Label |
|---|---|---|---|---|---|
| 1 | 1 | 1 | |||
| 1 | 1 | 1 | |||
| 2 | 1 | 1 | |||
| 3 | 1 | 1 | |||
| 4 | 1 | 1 | |||
| 5 | 1 | 1 | |||
| 6 | 1 | 1 | |||
| 2 | 2 | 2 | |||
| 7 | 1 | 1 | |||
| 8 | 1 | 1 | |||
| 9 | 1 | 1 | |||
| 10 | 1 | 1 | |||
| 11 | 1 | 1 | |||
| 12 | 1 | 1 |
Results Overview
Summary Table
| #Peptides Quantified | #Proteins Quantified |
|---|---|
| 3725 | 767 |
HeatMap
Pipeline Result Statistics
| Sample Name | MSstats_Condition | Fraction | #Peptide IDs | #Unambiguous Peptide IDs | #Modified Peptide IDs | #Protein (group) IDs |
|---|---|---|---|---|---|---|
| 1 | 1 | |||||
| 1 | 2871 | 2871 | 402 | 557 | ||
| 1 | 2877 | 2877 | 393 | 548 | ||
| 1 | 2513 | 2513 | 336 | 481 | ||
| 1 | 3001 | 3001 | 411 | 590 | ||
| 1 | 2941 | 2941 | 413 | 578 | ||
| 1 | 3020 | 3020 | 419 | 593 | ||
| 2 | 2 | |||||
| 1 | 2641 | 2641 | 350 | 522 | ||
| 1 | 2766 | 2766 | 361 | 563 | ||
| 1 | 3043 | 3043 | 408 | 615 | ||
| 1 | 2887 | 2887 | 387 | 580 | ||
| 1 | 2336 | 2336 | 313 | 456 | ||
| 1 | 2517 | 2517 | 340 | 509 |
Identification Summary
Number of Peptides identified Per Protein
ProteinGroups Count
Peptide ID Count
Modifications Per Raw File
Quantification Analysis
Peptides Quantification Table
| PeptideID | Protein Name | Peptide Sequence | Best Search Score | Average Intensity | 1 | 2 |
|---|---|---|---|---|---|---|
| 1 | SRP14_HUMAN | AAAAAAAAAPAAAATAPTTAATTAATAAQ | 0.9909 | 5.4381 | 5.4440 | 5.4321 |
| 2 | RL4_HUMAN | AAAAAAALQAK | 0.9996 | 4.6753 | 4.6488 | 4.7002 |
| 3 | CLPX_HUMAN | AAAAADLANR | 0.9991 | 4.3438 | 4.1951 | 4.4205 |
| 4 | RCC2_HUMAN | AAAAAWEEPSSGNGTAR | 0.9994 | 4.0407 | 3.9916 | 4.0847 |
| 5 | TRUB1_HUMAN | AAAAVVAAAAR | 0.9996 | 4.2186 | 4.2661 | 3.8443 |
| 6 | EDC4_HUMAN | AAADTLQGPMQAAYR | 0.9996 | 4.7220 | 4.7436 | 4.6935 |
| 7 | MCCA_HUMAN | AAAKESLCQAALGLILK | 0.9996 | 5.2532 | 5.1854 | 5.3119 |
| 8 | RBM39_HUMAN | AAAMANNLQK | 0.9988 | 4.0772 | 3.9697 | 4.1078 |
| 9 | TTC4_HUMAN | AAAQYYLGNFR | 0.9932 | 4.0021 | 4.0316 | 3.8990 |
| 10 | UBE3A_HUMAN | AACSAAAMEEDSEASSSR | 0.9996 | 4.5588 | 4.6875 | 4.3269 |
| 11 | XPO2_HUMAN | AADEEAFEDNSEEYIRR | 0.9977 | 4.7202 | 4.6946 | 4.7491 |
| 12 | RN213_HUMAN | AADFLSEPEGGPEMAK | 0.9996 | 5.3026 | 5.5332 | 4.5048 |
| 13 | RN213_HUMAN | AADFLSEPEGGPEMAKEK | 0.9990 | 5.0719 | 5.2717 | 4.1652 |
| 14 | SRRM2_HUMAN | AAFGISDSYVDGSSFDPQRR | 0.9996 | 5.2061 | 5.1766 | 5.2338 |
| 15 | SYAM_HUMAN | AAFLNFFR | 0.9996 | 5.4961 | 5.4827 | 5.5091 |
| 16 | PUR2_HUMAN | AAGFKDPLLASGTDGVGTK | 0.9986 | 4.1988 | 4.2102 | 4.1497 |
| 17 | SYTM_HUMAN | AAGLVSDLDADSGLTLSR | 0.9981 | 4.7433 | 4.7657 | 4.7197 |
| 18 | RLA1_HUMAN | AAGVNVEPFWPGLFAK | 0.9996 | 4.5872 | 4.6028 | 4.5710 |
| 19 | TCPB_HUMAN | AAHSEGNTTAGLDMR | 0.9924 | 4.3590 | 4.3935 | 4.2806 |
| 20 | FAS_HUMAN | AALQEELQLCK | 0.9990 | 4.5873 | 4.5966 | 4.5793 |
| 21 | RS25_HUMAN | AALQELLSK | 0.9996 | 5.1240 | 5.1337 | 5.1141 |
| 22 | ECHB_HUMAN | AALTGLLHR | 0.9990 | 4.2079 | 4.2243 | 4.1943 |
| 23 | TBB6_HUMAN | AALVDLEPGTMDSVR | 0.9996 | 4.8027 | 4.7921 | 4.8129 |
| 24 | ADPPT_HUMAN | AAMAGRLMIR | 0.9970 | 4.3440 | 4.3259 | 4.4095 |
| 25 | NU214_HUMAN | AAPGPGPSTFSFVPPSK | 0.9996 | 4.7709 | 4.7800 | 4.7631 |
| 26 | TBCD_HUMAN | AASAAFQENVGR | 0.9997 | 3.9786 | 3.9786 | |
| 27 | RN213_HUMAN | AASEAPEEEVSLPWVHLAYQR | 0.9996 | 5.3156 | 5.3156 | |
| 28 | TCOF_HUMAN | AASVPVKGSLGQGTAPVLPGK | 0.9996 | 4.5654 | 4.4186 | 4.6051 |
| 29 | MCCB_HUMAN | AATGEEVSAEDLGGADLHCR | 0.9982 | 4.4101 | 4.3451 | 4.4393 |
| 30 | DNJC7_HUMAN | AATLMMLGR | 0.9950 | 4.9647 | 4.9603 | 4.9691 |
| 31 | DYHC1_HUMAN | AATSPALFNR | 0.9997 | 4.0774 | 4.1210 | 3.9121 |
| 32 | UBA1_HUMAN | AAVATFLQSVQVPEFTPK | 0.9993 | 6.7711 | 6.8252 | 6.7093 |
| 33 | EDC3_HUMAN | AAVAWANQNR | 0.9997 | 3.9743 | 4.0032 | 3.8737 |
| 34 | CH60_HUMAN | AAVEEGIVLGGGCALLR | 0.9996 | 5.0614 | 5.0223 | 5.0973 |
| 35 | DPOG1_HUMAN | AAVPGQPLALTAR | 0.9996 | 4.7643 | 4.7132 | 4.8100 |
| 36 | FAKD5_HUMAN | AAVPLGGFLCNVADK | 0.9993 | 5.0217 | 5.0119 | 5.0360 |
| 37 | IRS4_HUMAN | AAVSAFPTDSLER | 0.9996 | 5.1675 | 5.2056 | 5.1256 |
| 38 | ADT2_HUMAN | AAYFGIYDTAK | 0.9996 | 5.0209 | 5.0403 | 5.0007 |
| 39 | ADT3_HUMAN | AAYFGVYDTAK | 0.9974 | 4.3526 | 4.3888 | 4.2992 |
| 40 | UBP11_HUMAN | AAYVLFYQR | 0.9996 | 4.5635 | 4.6816 | 4.2890 |
| 41 | DDX41_HUMAN | ACDESVLMDLK | 0.9968 | 4.3978 | 4.2691 | 4.4502 |
| 42 | NU214_HUMAN | ACFQVGTSEEMK | 0.9997 | 4.2240 | 4.2240 | |
| 43 | FAS_HUMAN | ACLDTAVENMPSLK | 0.9996 | 4.5301 | 4.5389 | 4.5211 |
| 44 | DAAF5_HUMAN | ACLQPSQDPQMR | 0.9996 | 4.3545 | 4.3545 | |
| 45 | RS3A_HUMAN | ACQSIYPLHDVFVR | 0.9994 | 3.9083 | 3.7995 | 3.9682 |
| 46 | PYC_HUMAN | ACTELGIR | 0.9949 | 6.3404 | 6.3142 | 6.3675 |
| 47 | RS3_HUMAN | ACYGVLR | 0.9996 | 4.1379 | 4.0071 | 4.1910 |
| 48 | PYC_HUMAN | ADEAYLIGR | 0.9996 | 6.4957 | 6.4781 | 6.5126 |
| 49 | PRDX1_HUMAN | ADEGISFR | 0.9963 | 5.0024 | 5.0223 | 4.9772 |
| 50 | PYC_HUMAN | ADFAQACQDAGVR | 0.9996 | 7.0529 | 7.0255 | 7.0786 |
Protein Quantification Table
| ProteinID | Protein Name | Number of Peptides | Average Intensity | 1 | 2 |
|---|---|---|---|---|---|
| 1 | 1433T_HUMAN | 3 | 4.7074 | 4.7155 | 4.7005 |
| 2 | 2A5D_HUMAN | 2 | 4.3485 | 4.4411 | 4.2108 |
| 3 | 3MG_HUMAN | 2 | 4.3551 | 4.4182 | 4.2709 |
| 4 | 4ET_HUMAN | 1 | 4.6145 | 4.5966 | 4.6289 |
| 5 | AAAS_HUMAN | 1 | 4.2397 | 4.1921 | 4.2574 |
| 6 | AAAT_HUMAN | 1 | 4.0604 | 3.9195 | 4.1666 |
| 7 | AACS_HUMAN | 2 | 4.3285 | 4.4233 | 4.1704 |
| 8 | AAPK1_HUMAN | 2 | 4.2435 | 4.2944 | 4.0687 |
| 9 | AASS_HUMAN | 2 | 4.1258 | 4.1258 | |
| 10 | ABCF3_HUMAN | 1 | 4.1532 | 4.1532 | |
| 11 | ACACA_HUMAN | 218 | 6.4298 | 6.4275 | 6.4321 |
| 12 | ACACB_HUMAN | 84 | 5.3517 | 5.3085 | 5.3902 |
| 13 | ACADM_HUMAN | 3 | 4.3018 | 4.0664 | 4.3156 |
| 14 | ACDSB_HUMAN | 1 | 4.6824 | 4.7100 | 4.6606 |
| 15 | ACLY_HUMAN | 3 | 4.2730 | 4.1253 | 4.3544 |
| 16 | ACSF2_HUMAN | 9 | 4.4159 | 4.4001 | 4.4315 |
| 17 | ACSF3_HUMAN | 2 | 4.6234 | 4.6688 | 4.5781 |
| 18 | ACSL3_HUMAN | 2 | 4.1244 | 3.5794 | 4.2172 |
| 19 | ACTB_HUMAN;ACTG_HUMAN | 12 | 5.0384 | 4.8963 | 5.1044 |
| 20 | ADPPT_HUMAN | 1 | 4.3440 | 4.3259 | 4.4095 |
| 21 | ADRM1_HUMAN | 1 | 4.0016 | 4.0016 | |
| 22 | ADRO_HUMAN | 6 | 4.4665 | 4.3656 | 4.5260 |
| 23 | ADT2_HUMAN | 12 | 5.2115 | 5.2239 | 5.1990 |
| 24 | ADT3_HUMAN | 2 | 5.0502 | 5.0404 | 5.0609 |
| 25 | AFG2H_HUMAN;PRS8_HUMAN | 1 | 4.3273 | 4.0658 | 4.3738 |
| 26 | AHSA1_HUMAN | 3 | 4.0511 | 3.8600 | 4.0726 |
| 27 | AIFM3_HUMAN | 1 | 4.5212 | 4.5670 | 4.4588 |
| 28 | AIP_HUMAN | 1 | 4.7044 | 4.7467 | 4.6673 |
| 29 | AL3A2_HUMAN | 1 | 4.0519 | 4.0519 | |
| 30 | ALBU_HUMAN | 5 | 5.4180 | 5.4045 | 5.4307 |
| 31 | ALDOA_HUMAN | 7 | 4.4211 | 4.1970 | 4.4860 |
| 32 | ALDOC_HUMAN | 1 | 5.5951 | 5.6728 | 5.5005 |
| 33 | AMPD1_HUMAN | 1 | 4.1645 | 4.1645 | |
| 34 | ANKH1_HUMAN | 25 | 4.7226 | 4.6686 | 4.7627 |
| 35 | ANM3_HUMAN | 1 | 4.2971 | 4.3216 | 4.2711 |
| 36 | ANXA2_HUMAN | 2 | 4.4899 | 4.4994 | 4.4784 |
| 37 | ARAF_HUMAN;BRAF_HUMAN;RAF1_HUMAN | 1 | 4.2792 | 4.2792 | |
| 38 | ARFG1_HUMAN | 1 | 4.2983 | 4.3421 | 4.1318 |
| 39 | ARGL1_HUMAN | 6 | 4.9927 | 4.9777 | 5.0068 |
| 40 | ARHG2_HUMAN | 9 | 4.5272 | 4.5799 | 4.4636 |
| 41 | ARHG6_HUMAN;ARHG7_HUMAN | 1 | 4.3469 | 4.3692 | 4.2722 |
| 42 | ARHGB_HUMAN | 1 | 4.4778 | 4.4778 | |
| 43 | ARI1_HUMAN | 4 | 4.7339 | 4.8060 | 4.6313 |
| 44 | ARI2_HUMAN | 2 | 4.3654 | 4.3958 | 4.2973 |
| 45 | ARMC6_HUMAN | 3 | 4.2247 | 4.2407 | 4.0815 |
| 46 | ASCC2_HUMAN | 1 | 4.6552 | 4.7229 | 4.5750 |
| 47 | ASCC3_HUMAN | 8 | 4.5224 | 4.5540 | 4.4751 |
| 48 | ASNS_HUMAN | 9 | 4.7458 | 4.7941 | 4.5946 |
| 49 | ASTRA_HUMAN | 1 | 4.7560 | 4.8323 | 4.5454 |
| 50 | AT1A1_HUMAN;AT1A3_HUMAN | 2 | 4.5193 | 4.3879 | 4.5969 |
Intensity Distribution
Standard Deviation of Intensity
MS1 Analysis
Total Ion Chromatograms
MS1 Base Peak Chromatograms
MS1 Peaks
General stats for MS1 information
| File | Acquisition Date Time | log10(Total Current) | log10(Scan Current) |
|---|---|---|---|
| 20221028_FL_Lu_SV_Set12_A1 | 2022-10-29 22:11:31 | 11.7957 | 11.3888 |
| 20221028_FL_Lu_SV_Set12_A2 | 2022-10-30 01:33:52 | 11.8052 | 34.2775 |
| 20221028_FL_Lu_SV_Set12_A3 | 2022-10-30 13:47:37 | 11.7305 | 11.3256 |
| 20221028_FL_Lu_SV_Set12_A4 | 2022-10-30 06:40:43 | 11.8220 | 11.4029 |
| 20221028_FL_Lu_SV_Set12_A5 | 2022-10-30 09:03:01 | 11.8009 | 11.3846 |
| 20221028_FL_Lu_SV_Set12_A6 | 2022-10-30 01:56:09 | 11.8099 | 11.4013 |
| 20221028_FL_Lu_SV_Set12_B1 | 2022-10-29 12:42:17 | 11.7506 | 11.3651 |
| 20221028_FL_Lu_SV_Set12_B2 | 2022-10-30 11:25:17 | 11.8033 | 11.3784 |
| 20221028_FL_Lu_SV_Set12_B3 | 2022-10-29 15:04:34 | 11.8335 | 11.4320 |
| 20221028_FL_Lu_SV_Set12_B4 | 2022-10-30 04:18:27 | 11.8097 | 11.4051 |
| 20221028_FL_Lu_SV_Set12_B5 | 2022-10-29 17:26:54 | 11.6971 | 11.3046 |
| 20221028_FL_Lu_SV_Set12_B6 | 2022-10-29 19:49:11 | 11.7172 | 11.3146 |